httpgd can't find libpng dependencies during install in AL2023 Docker image

[jimgar]

Describe the bug

First of all, thank you for this package. I switched to VS Code as my main R IDE in December and it's been fun and productive - partly thanks to this package's existence. So I really appreciate all the hard work that must go into its development and maintenance.

As for the 'bug', if it is one: When installing httpgd in an AL2023:provided base Docker image, either from CRAN or the dev version, the following error occurs at the end

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R/4.3.2/lib/R/library/unigd/libs/unigd.so':
  libpng15.so.15: cannot open shared object file: No such file or directory

To Reproduce

1. Either build & exec into the container of the below Dockerfile, or use the below devcontainer.json and build the container in e.g. VS Code
2. Launch an R session
3. Run install.packages("httpgd")

Dockerfile

FROM public.ecr.aws/lambda/provided:latest-x86_64

ENV R_VERSION=4.3.2

RUN dnf -y install glibc-langpack-en \
    # General system requirements 
    wget \
    git \
    tar \
    # System requirements for R packages
    # httpgd
    fontconfig-devel \
    freetype-devel \
    cairo-devel \
    libpng-devel \
    # unigd
    libtiff-devel 

RUN wget https://cdn.rstudio.com/r/rhel-9/pkgs/R-${R_VERSION}-1-1.x86_64.rpm

# System requirements for R
RUN dnf install -y `rpm -qR R-${R_VERSION}-1-1.x86_64.rpm | tr '\n' ' ' `

RUN rpm -i R-${R_VERSION}-1-1.x86_64.rpm \
    && rm R-${R_VERSION}-1-1.x86_64.rpm

ENV PATH="${PATH}:/opt/R/${R_VERSION}/bin/"

RUN Rscript -e "install.packages(c( \ 
    'httpgd', \
    'languageserver' \
    ), repos = 'https://packagemanager.rstudio.com/all/__linux__/centos7/latest')" 

devcontainer.json

{
  "name": "R Dev Environment",
  "build": {
    "dockerfile": "Dockerfile.dev"
  },
  "customizations": {
    "vscode": {
      "settings": {
        // Annoying bug in VS Code means we have to set specify extensions.verifySignature to false.
        // Otherwise extensions will not install, which is part of the point of having a devcontainer!
        // See https://github.com/microsoft/vscode/issues/175705
        "extensions.verifySignature": false,
        "[r]": {
          "editor.formatOnSave": true,
          "editor.tabSize": 2,
          "editor.detectIndentation": false
        },
        "r.bracketedPaste": true,
        "r.rpath.linux": "/opt/R/4.3.2/bin/R",
        "r.rterm.option": [
          "--no-save",
          "--no-restore",
          "--r-binary=/opt/R/4.3.2/bin/R"
        ],
        "r.plot.useHttpgd": true,
        "r.sessionWatcher": true,
        "r.workspaceViewer.removeHiddenItems": true,
        "editor.formatOnSave": true
      },
      "extensions": [
        // R
        "reditorsupport.r",
        // Docker syntax highlighting etc
        "ms-azuretools.vscode-docker"
      ]
    }
  }
}

Expected behavior

httpgd installs successfully 🥲

Environment

• OS: macOS Sonoma 14.4.1, M1 chip
• Browser: Chrome
• R version: 4.3.2
• httpgd version: 2.0.1

Additional context

The Dockerfile is a much slimmed down version of my actual one, which is a developer environment for an AWS lambda where the CDK is written in Python and the lambda process is in R. I more or less need to use this image for that reason, so I'm stuck with the AL2023 frankendistro. This is the most minimal reprex that I could come up with.

As you can see the build includes installing all the system dependencies for unigd and httpgd, i.e. fontconfig-devel, freetype-devel, cairo-devel, libpng-devel, and libtiff-devel. I also think libpng is installing successfully but (see below) it's version 16, where httpgd seems to be looking for version 15? I can't find a way to downgrade - here's a link to the available packages for AL2023, if that's helpful.

find / -name libpng*
/usr/lib64/pkgconfig/libpng16.pc
/usr/lib64/pkgconfig/libpng.pc
/usr/lib64/libpng16.so
/usr/lib64/libpng.so
/usr/lib64/libpng16.so.16.37.0
/usr/lib64/libpng16.so.16
/usr/include/libpng16
/usr/bin/libpng16-config
/usr/bin/libpng-config
/usr/share/man/man3/libpngpf.3.gz
/usr/share/man/man3/libpng.3.gz
/usr/share/doc/libpng-devel
/usr/share/doc/libpng-devel/libpng-manual.txt
/usr/share/licenses/libpng
find: ‘/proc/11226’: No such file or directory
find: ‘/proc/11227’: No such file or directory
find: ‘/proc/11232’: No such file or directory
find: ‘/proc/11233’: No such file or directory

Might be worth mentioning that unigd installs successfully.

> packageVersion("unigd")
[1] ‘0.1.1’

Full log when attempting installation

> install.packages("httpgd")
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/httpgd_2.0.1.tar.gz'
Content type 'application/x-gzip' length 335606 bytes (327 KB)
==================================================
downloaded 327 KB

* installing *source* package ‘httpgd’ ...
** package ‘httpgd’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
using C++14
rm -f httpgd.so cpp11.o httpgd.o httpgd_rng.o httpgd_webserver.o unigd_impl.o
g++ -std=gnu++14 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Ilib -DFMT_HEADER_ONLY -I'/opt/R/4.3.2/lib/R/library/unigd/include' -I'/opt/R/4.3.2/lib/R/library/cpp11/include' -I'/opt/R/4.3.2/lib/R/library/AsioHeaders/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++14 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Ilib -DFMT_HEADER_ONLY -I'/opt/R/4.3.2/lib/R/library/unigd/include' -I'/opt/R/4.3.2/lib/R/library/cpp11/include' -I'/opt/R/4.3.2/lib/R/library/AsioHeaders/include' -I/usr/local/include    -fpic  -g -O2  -c httpgd.cpp -o httpgd.o
g++ -std=gnu++14 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Ilib -DFMT_HEADER_ONLY -I'/opt/R/4.3.2/lib/R/library/unigd/include' -I'/opt/R/4.3.2/lib/R/library/cpp11/include' -I'/opt/R/4.3.2/lib/R/library/AsioHeaders/include' -I/usr/local/include    -fpic  -g -O2  -c httpgd_rng.cpp -o httpgd_rng.o
g++ -std=gnu++14 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Ilib -DFMT_HEADER_ONLY -I'/opt/R/4.3.2/lib/R/library/unigd/include' -I'/opt/R/4.3.2/lib/R/library/cpp11/include' -I'/opt/R/4.3.2/lib/R/library/AsioHeaders/include' -I/usr/local/include    -fpic  -g -O2  -c httpgd_webserver.cpp -o httpgd_webserver.o
g++ -std=gnu++14 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Ilib -DFMT_HEADER_ONLY -I'/opt/R/4.3.2/lib/R/library/unigd/include' -I'/opt/R/4.3.2/lib/R/library/cpp11/include' -I'/opt/R/4.3.2/lib/R/library/AsioHeaders/include' -I/usr/local/include    -fpic  -g -O2  -c unigd_impl.cpp -o unigd_impl.o
g++ -std=gnu++14 -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o httpgd.so cpp11.o httpgd.o httpgd_rng.o httpgd_webserver.o unigd_impl.o -L/opt/R/4.3.2/lib/R/lib -lR
installing to /opt/R/4.3.2/lib/R/library/00LOCK-httpgd/00new/httpgd/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R/4.3.2/lib/R/library/unigd/libs/unigd.so':
  libpng15.so.15: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘httpgd’
* removing ‘/opt/R/4.3.2/lib/R/library/httpgd’

The downloaded source packages are in
        ‘/tmp/RtmpnJMYjd/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("httpgd") :
  installation of package ‘httpgd’ had non-zero exit status

Please let me know if there's any more info I can give or things to try. I may need a little advice as I'm out of my comfort zone but will do my best to work with you, if you can help :)

Best,
Jim

[eitsupi]

Why not use rig for R installation and pak for R package installation? If you use pak on a Linux distribution like RHEL, the dependent system packages will be installed automatically and you will not need to install them manually.

[nx10]

I second that pak might be worth a try but in general there seems something wrong with the R c++ build setup. Is httpgd/unigd the only source package you have trouble with? Updating all the build tools (GCC, make, ...) might be worth a try. I think the rocker (Ubuntu based) images build R from source.

Edit: it might also be worth to ask over at lambdr

[jimgar]

Hi both, thanks for the replies!

Why not use rig for R installation and pak for R package installation? If you use pak on a Linux distribution like RHEL, the dependent system packages will be installed automatically and you will not need to install them manually.

@eitsupi, this is a good question. Honestly, it didn't cross my mind. I've never had a need to use either of these before because we haven't had lambdas running R processes - we just do our thing on macbooks. System dependencies are ours to resolve individually.

I've looked into it though and the answer is that pak doesn't resolve system requirements for the AL2023 distro, which is not a standard Linux distro but rather a bespoke one that AWS has made. I installed pak in the container and ran pak::sysreqs_is_supported(), which returned FALSE. Also, pak doesn't seem to support installing specific versions of packages from what I can tell, and I want that to be able to pin versions for production. But please correct me if I'm wrong on that.

I second that pak might be worth a try but in general there seems something wrong with the R c++ build setup. Is httpgd/unigd the only source package you have trouble with? Updating all the build tools (GCC, make, ...) might be worth a try. I think the rocker (Ubuntu based) images build R from source.

Edit: it might also be worth to ask over at lambdr

@nx10 unigd seems to install fine, and so did pak and its dependencies which all installed from source (see below).

I've only observed the issue with httpgd. I added gcc and make-devel to the container but it didn't make a difference.

Any other ideas about the tool chain?

pak compiling from source

> install.packages("pak")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/pak_0.7.2.tar.gz'
Content type 'application/x-gzip' length 2027490 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

* installing *source* package ‘pak’ ...
** package ‘pak’ successfully unpacked and MD5 sums checked
** using staged installation
** Running ./configure
** libs
Current platform: x86_64-pc-linux-gnu 
Build platform:   
Target platform:   

Compiling R6 

Compiling cli 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/cli/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c ansi.c -o ansi.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c cleancall.c -o cleancall.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c diff.c -o diff.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c errors.c -o errors.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c glue.c -o glue.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c inst.c -o inst.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c keypress-unix.c -o keypress-unix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c keypress-win.c -o keypress-win.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c keypress.c -o keypress.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c md5.c -o md5.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c progress-altrep.c -o progress-altrep.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c progress.c -o progress.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c sha1.c -o sha1.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c sha256.c -o sha256.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c thread.c -o thread.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c tty.c -o tty.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c utf8.c -o utf8.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c vt.c -o vt.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c vtparse.c -o vtparse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c vtparse_table.c -o vtparse_table.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c win-utf8.c -o win-utf8.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -c winfiles.c -o winfiles.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/cli/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/cli/libs

Compiling curl 
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/curl/src'
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c callbacks.c -o callbacks.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c curl.c -o curl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c download.c -o download.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c escape.c -o escape.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c fetch.c -o fetch.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c findport.c -o findport.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c form.c -o form.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c getdate.c -o getdate.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c handle.c -o handle.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ieproxy.c -o ieproxy.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c interrupt.c -o interrupt.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c multi.c -o multi.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c nslookup.c -o nslookup.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c options.c -o options.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c reflist.c -o reflist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c split.c -o split.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ssl.c -o ssl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c typechecking.c -o typechecking.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c version.c -o version.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c winidn.c -o winidn.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c writer.c -o writer.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/curl/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/curl/libs

Compiling filelock 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/filelock/src'
rm -f filelock.so init.o filelock-unix.o locklist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c filelock-unix.c -o filelock-unix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c locklist.c -o locklist.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o filelock.so init.o filelock-unix.o locklist.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/filelock/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/filelock/libs

Compiling jsonlite 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/jsonlite/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_array.c -o collapse_array.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_object.c -o collapse_object.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c escape_chars.c -o escape_chars.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_datelist.c -o is_datelist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_recordlist.c -o is_recordlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c null_to_na.c -o null_to_na.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c num_to_char.c -o num_to_char.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c parse.c -o parse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c prettify.c -o prettify.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c push_parser.c -o push_parser.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c r-base64.c -o r-base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c register.c -o register.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c row_collapse.c -o row_collapse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c transpose_list.c -o transpose_list.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c validate.c -o validate.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/jsonlite/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/jsonlite/libs
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”

Compiling lpSolve 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/lpSolve/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c colamd.c -o colamd.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c commonlib.c -o commonlib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c hbio.c -o hbio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c ini.c -o ini.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c isfixedvar.c -o isfixedvar.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_Hash.c -o lp_Hash.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_LUSOL.c -o lp_LUSOL.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_MDO.c -o lp_MDO.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_MPS.c -o lp_MPS.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_SOS.c -o lp_SOS.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_crash.c -o lp_crash.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_lib.c -o lp_lib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_matrix.c -o lp_matrix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_mipbb.c -o lp_mipbb.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_params.c -o lp_params.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_presolve.c -o lp_presolve.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_price.c -o lp_price.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_pricePSE.c -o lp_pricePSE.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_report.c -o lp_report.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_rlp.c -o lp_rlp.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_scale.c -o lp_scale.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_simplex.c -o lp_simplex.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_utils.c -o lp_utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lp_wlp.c -o lp_wlp.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lpslink56.c -o lpslink56.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lusol.c -o lusol.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c lusolio.c -o lusolio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c mmio.c -o mmio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c myblas.c -o myblas.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c sparselib.c -o sparselib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -c yacc_read.c -o yacc_read.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o lpSolve.so colamd.o commonlib.o hbio.o ini.o init.o isfixedvar.o lp_Hash.o lp_LUSOL.o lp_MDO.o lp_MPS.o lp_SOS.o lp_crash.o lp_lib.o lp_matrix.o lp_mipbb.o lp_params.o lp_presolve.o lp_price.o lp_pricePSE.o lp_report.o lp_rlp.o lp_scale.o lp_simplex.o lp_utils.o lp_wlp.o lpslink56.o lusol.o lusolio.o mmio.o myblas.o sparselib.o yacc_read.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/lpSolve/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/lpSolve/libs

Compiling ps 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/ps/src'
gcc -g -O2  -L/usr/local/lib -Wall px.c -o px
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-common.c -o api-common.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c common.c -o common.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c extra.c -o extra.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dummy.c -o dummy.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c error-codes.c -o error-codes.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c posix.c -o posix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-posix.c -o api-posix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c linux.c -o linux.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-linux.c -o api-linux.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/ps/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/ps

Compiling zip 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/zip/src'
gcc -g -O2  miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
gcc -g -O2  miniz.c zip.c unixutils.c tools/cmdunzip.c -o tools/cmdunzip
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c miniz.c -o miniz.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rzip.c -o rzip.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c zip.c -o zip.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c unixutils.c -o unixutils.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/zip/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/zip

Compiling processx 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/processx/src'
gcc -g -O2  -L/usr/local/lib -Wall tools/px.c -o tools/px
gcc -g -O2  -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock
gcc -g -O2  -L/usr/local/lib supervisor/supervisor.c \
      supervisor/utils.c -o supervisor/supervisor
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c client.c -o client.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c errors.c -o errors.o
gcc -shared -L"/opt/R/4.3.2/lib/R/lib" -L/usr/local/lib -o client.so base64.o client.o errors.o  \
         -L"/opt/R/4.3.2/lib/R/lib" -lR
if [ -n "" ]; then \
    echo Removing libR.so dependency from client.so; \
    patchelf --remove-needed libR.so client.so; \
fi
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c poll.c -o poll.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c processx-connection.c -o processx-connection.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c processx-vector.c -o processx-vector.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c create-time.c -o create-time.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/childlist.c -o unix/childlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/connection.c -o unix/connection.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/processx.c -o unix/processx.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/sigchld.c -o unix/sigchld.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/utils.c -o unix/utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c unix/named_pipe.c -o unix/named_pipe.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c cleancall.c -o cleancall.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/processx/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/processx

Compiling callr 

Compiling desc 

Compiling pkgbuild 

Compiling pkgcache 
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/pkgcache/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c errors.c -o errors.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lib.c -o lib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c winfiles.c -o winfiles.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o pkgcache.so errors.o init.o lib.o winfiles.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/pkgcache/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/pkgcache/libs

Compiling pkgsearch 

Compiling pkgdepends 
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘pak’
    finding HTML links ... done
    cache                                   html  
    faq                                     html  
    features                                html  
    get-started                             html  
    handle_package_not_found                html  
    install                                 html  
    lib_status                              html  
    local_deps                              html  
    local_deps_explain                      html  
    local_install                           html  
    local_install_deps                      html  
    local_install_dev_deps                  html  
    local_package_trees                     html  
    local_system_requirements               html  
    lockfile_create                         html  
    lockfile_install                        html  
    metadata                                html  
    package-dependency-types                html  
    pak-config                              html  
    pak-package                             html  
    pak                                     html  
    pak_cleanup                             html  
    pak_install_extra                       html  
    pak_package_sources                     html  
    pak_setup                               html  
    pak_sitrep                              html  
    pak_solver                              html  
    pak_update                              html  
    pkg_deps                                html  
    pkg_deps_explain                        html  
    pkg_deps_tree                           html  
    pkg_download                            html  
    pkg_history                             html  
    pkg_install                             html  
    pkg_name_check                          html  
    pkg_remove                              html  
    pkg_search                              html  
    pkg_status                              html  
    pkg_sysreqs                             html  
    ppm_has_binaries                        html  
    ppm_platforms                           html  
    ppm_r_versions                          html  
    ppm_repo_url                            html  
    ppm_snapshots                           html  
    repo_add                                html  
    repo_get                                html  
    repo_status                             html  
    sysreqs                                 html  
    sysreqs_check_installed                 html  
    sysreqs_db_list                         html  
    sysreqs_db_match                        html  
    sysreqs_db_update                       html  
    sysreqs_is_supported                    html  
    sysreqs_list_system_packages            html  
    sysreqs_platforms                       html  
    system_r_platform                       html  
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pak)
Making 'packages.html' ... done

The downloaded source packages are in
        ‘/tmp/Rtmp2lvTI7/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

[jimgar]

Ok, I've got a solution.

I think the issue here, ultimately, is that AWS have their own lightweight distro of Linux. It's an RPM-based distro, but not directly comparable to any Fedora release, CentOS, or RHEL. From there, my lack of confidence and understanding caused the mess. I had the RHEL 9 version of R installing, but was then attempting to install R packages from the CentOS 7 Posit Package Manager repo. Total mismatch.

I changed the R package installation to look like the below, bringing it in line with the R version, and now it's all good.

RUN Rscript -e "install.packages(c( \
    'httpgd', \
    'jsonlite', \
    'languageserver' \
    ), repos = 'https://packagemanager.posit.co/cran/__linux__/rhel9/2024-04-08')"

Not really sure if I should be using RHEL 9 or CentOS 7. But certainly using RHEL 9 has sorted out the httpgd install, so I'm going to go ahead and close this. Thanks again for the package and best wishes!